[English] 日本語
![](img/lk-miru.gif)
- PDB-2f5d: Bacillus subtilis manganese transport regulator (MNTR) bound to m... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2f5d | ||||||
---|---|---|---|---|---|---|---|
Title | Bacillus subtilis manganese transport regulator (MNTR) bound to manganese, AC conformation, pH 6.5 | ||||||
![]() | Transcriptional regulator mntR | ||||||
![]() | TRANSCRIPTION / HELIX-TURN-HELIX / DNA-BINDING PROTEIN / METALLOREGULATORY PROTEIN | ||||||
Function / homology | ![]() intracellular manganese ion homeostasis / manganese ion binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kliegman, J.I. / Griner, S.L. / Helmann, J.D. / Brennan, R.G. / Glasfeld, A. | ||||||
![]() | ![]() Title: Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis. Authors: Kliegman, J.I. / Griner, S.L. / Helmann, J.D. / Brennan, R.G. / Glasfeld, A. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE AUTHOR MAINTAINS THAT THE CORRECT RESIDUE AT THIS LOCATION SHOULD BE GLU. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 67.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 443 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ev0C ![]() 2ev5C ![]() 2ev6C ![]() 2f5cC ![]() 2f5eC ![]() 2f5fC ![]() 1on1S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16787.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.55 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 4000, 0.1 M MAGNESIUM CHLORIDE, 0.1 M CACODYLATE, PH 6.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K |
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 3, 2003 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31.5 Å / Num. obs: 25228 / % possible obs: 90 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.9→2.02 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.5 / % possible all: 61.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ON1 Resolution: 1.9→31.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1466646.21 / Data cutoff high rms absF: 1466646.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.4239 Å2 / ksol: 0.340365 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|